Serra M J, Lyttle M H, Axenson T J, Schadt C A, Turner D H
Department of Chemistry, Allegheny College, Meadville, PA 16335.
Nucleic Acids Res. 1993 Aug 11;21(16):3845-9. doi: 10.1093/nar/21.16.3845.
Thermodynamic parameters are reported for hairpin formation in 1 M NaCl by RNA sequences of the type GGXAUAAUAYCC, where X and Y are CG, GC, AU, UA, GU, or UG. A nearest neighbor analysis of the data indicates the free energy change for loop formation at 37 degrees C, delta degrees Gl,37, averages 3.4 kcal/mol for hairpin loops closed with C.G, G.C, and G.U pairs. In contrast, delta G degree l,37 averages 4.6 kcal/mol for loops closed with A.U, U.A, or U.G pairs. Thus the stability of an RNA hairpin depends on the closing base pair. The hairpin with a GA mismatch that is formed by GGCGUAAUAGCC is more stable than the corresponding hairpin with an AA mismatch. Thus hairpin stability also depends on loop sequence. These effects are not included in current algorithms for prediction of RNA structure from sequence.
报道了在1M NaCl中，由GGXAUAAUAYCC类型的RNA序列形成发夹结构的热力学参数，其中X和Y为CG、GC、AU、UA、GU或UG。对数据的最近邻分析表明，在37℃时形成环的自由能变化，即ΔG°l,37，对于由C.G、G.C和G.U碱基对封闭的发夹环平均为3.4千卡/摩尔。相比之下，对于由A.U、U.A或U.G碱基对封闭的环，ΔG°l,37平均为4.6千卡/摩尔。因此，RNA发夹的稳定性取决于封闭碱基对。由GGCGUAAUAGCC形成的具有GA错配的发夹比具有AA错配的相应发夹更稳定。因此，发夹稳定性还取决于环序列。这些效应未包含在当前从序列预测RNA结构的算法中。
